Proper control of gene expression is essential for life. While substantial advances have been made in the discovery of DNA sequences and transcription factors that act combinatorial to regulate transcription, much less is known about later steps in the gene expression program. Nevertheless, it is now clear that substantial regulation and gene expression occurs post-transcriptional, in pre-mRNA splicing, RNA transport, RNA localization, translation, and RNA decay, and in the coordination of RNAs by RNA binding proteins (RBPs). Further, recent findings of widespread transcription of noncoding RNAs (ncRNA) and of the involvement of these RNAs in critical biological processes such as development and gene regulation suggest the existence of important classes of regulatory RNAs that we are just beginning to explore. The long term goal of this project is to develop tools that enable structural characterization of RNAs on a genome-wide scale. First, we will develop computational methods to delineate functional motifs in RNA based on predicted secondary structures. Second, we will develop high-throughput methodologies of mapping secondary and tertiary structures in RNA using a series of RNA footprinting techniques and high resolution tiling array technology. Third, we will develop computational and experimental methods to assign biological functions to RNA motifs and to validate them. This integrated pipeline of new experimental and computational tools will enable investigators to identify and decode regulatory RNA elements in the genome with unprecedented speed and precision. The control of gene expression lies at the heart of understanding fundamental biological processes, such as cell growth, differentiation, and death. A deep and comprehensive understanding of the gene expression program would help to reveal the mechanisms of many human diseases exhibiting faulty gene expression, and allow their diagnosis and intervention with newfound precision.